Variant report

Variant	rs561454
Chromosome Location	chr4:74766726-74766727
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:74766463..74768421-chr4:74779822..74782631,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10007826	0.82[ASN][1000 genomes]
rs1366946	0.82[ASN][1000 genomes]
rs1366949	0.82[ASN][1000 genomes]
rs16850137	0.81[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2115691	0.96[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2145615	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2367291	0.83[GIH][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap]
rs2367293	0.82[ASN][1000 genomes]
rs24772	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28404022	0.83[EUR][1000 genomes]
rs2886927	0.83[GIH][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap]
rs2886969	0.85[EUR][1000 genomes]
rs2886970	0.85[EUR][1000 genomes]
rs2968710	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3097409	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3097411	0.96[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs3097412	0.81[ASW][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3111694	0.83[GIH][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap]
rs3111697	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3111698	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3117597	0.84[JPT][hapmap];0.83[YRI][hapmap]
rs3117598	0.83[GIH][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap]
rs3117600	0.83[GIH][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap]
rs3117604	0.85[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap]
rs4074	0.87[JPT][hapmap];0.83[MEX][hapmap]
rs482239	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs492155	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs493091	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs508977	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs512606	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs516224	0.81[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs518632	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs519565	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs537373	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs541923	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs548068	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs551744	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs562213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569390	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs573878	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs593641	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs596352	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs623659	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs634304	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs638767	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs654871	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs655328	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs673038	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs680044	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs680452	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs683671	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs684080	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6858086	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs7692638	0.83[EUR][1000 genomes]
rs9991272	0.91[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001725	chr4:74354050-74860924	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530126	chr4:74376622-74843892	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv432612	chr4:74723372-74774372	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs561454	CXCL6	cis	parietal	SCAN
rs561454	SEPT11	cis	parietal	SCAN
rs561454	FAM47E	cis	parietal	SCAN
rs561454	THOC1	trans	parietal	SCAN
rs561454	APBB3	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74757200-74770400	Enhancers	NHDF-Ad	bronchial
2	chr4:74759800-74770400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:74760200-74767000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:74761200-74767400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:74761200-74768600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:74761800-74766800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:74763200-74767600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:74763800-74767200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:74764200-74766800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:74765800-74768400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:74766400-74768400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:74766400-74768800	Enhancers	Osteobl	bone
13	chr4:74766600-74767200	Enhancers	K562	blood
14	chr4:74766600-74767200	Enhancers	NHLF	lung
15	chr4:74766600-74768600	Enhancers	HSMM	muscle
16	chr4:74766600-74768800	Enhancers	Muscle Satellite Cultured Cells	--

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